Setup Guide: R and RStudio for Stock Assessment Training

Somali Fish Stock Training

Authors

Affiliations

Masumbuko Semba

Nelson Mandela African Institution of Science and Technology

Rushingisha George

Tanzania Fisheries Research Institute

Mathew Silas

Deep Sea Fishing Authority

Introduction

This guide provides step-by-step instructions for installing the necessary software for our training session on length-based stock assessment. We will install:

1. R: The programming language for statistical computing and data analysis.
2. RStudio or Positron: An Integrated Development Environment (IDE) that makes working with R much easier and more user-friendly.
3. R Packages: Specialized add-ons for R that provide pre-built functions for data manipulation, visualization, and stock assessment analysis.

The Three Layers of the R Ecosystem

graph TB
    subgraph Layer3["<b>PACKAGES</b><br/>(Specialized Tools)"]
        direction LR
        P1["tidyverse<br/>(Data Wrangling)"]
        P2["LBSPR<br/>(Stock Assessment)"]
        P3["TropFishR<br/>(Fisheries Methods)"]
        P4["gt<br/>(Professional Tables)"]
    end
    
    subgraph Layer2["<b>IDE</b><br/>(User Interface)"]
        direction LR
        I1["RStudio<br/>(Popular & Easy)"]
        I2["OR"]
        I3["Positron<br/>(Modern & Flexible)"]
    end
    
    subgraph Layer1["<b>R</b><br/>(Foundation Engine)"]
        R["Statistical Programming Language"]
    end
    
    Layer3 --> Layer2
    Layer2 --> Layer1
    
    style Layer1 fill:#bbdefb
    style Layer2 fill:#fff9c4
    style Layer3 fill:#c8e6c9

Why do we need all three?

• R is the engine that does the actual computation
• IDE is the comfortable driver’s seat with a dashboard (RStudio or Positron)
• Packages are specialized tools that solve specific problems (no need to code everything from scratch)

Please follow these steps before the training session begins. The entire setup typically takes 30-60 minutes depending on your internet speed.

---

Step 1: Install R

What is R? R is a free, open-source programming language specifically designed for statistical computing and data analysis. It’s the foundation that everything else depends on.

Why install it first? RStudio and Positron are interfaces to R—they won’t work without R installed on your computer.

graph LR
    Start["<b>Your Computer</b>"] 
    Empty["No R installed"]
    Start --> Empty
    Empty -->|Step 1| RInstalled["<b>R Installed</b><br/>Foundation Ready"]
    RInstalled -->|Step 2| IDE["<b>IDE Installed</b><br/>User Interface Ready"]
    IDE -->|Step 3| Packages["<b>Packages Installed</b><br/>Tools Ready"]
    Packages -->|Step 4| Verify["<b>Verified & Ready!</b>"]
    
    style Start fill:#e1f5fe
    style RInstalled fill:#bbdefb
    style IDE fill:#fff9c4
    style Packages fill:#c8e6c9
    style Verify fill:#a5d6a7

Installation steps:

1. Go to the Comprehensive R Archive Network (CRAN) website: https://cran.r-project.org/

2. Look for the large download button and click on the link for your operating system:

   • Download R for Windows (if you use Windows)
   • Download R for macOS (if you use Mac)
   • Download R for Linux (if you use Linux)

3. Select the “base” distribution (this is the standard R package—other options are for advanced users).

4. Run the downloaded installer file:

   • Windows: Double-click the .exe file
   • macOS: Double-click the .pkg file
   • Linux: Follow the terminal instructions

5. Follow the on-screen prompts. You can safely accept all default settings—there’s no need to customize anything.

6. Once installation completes, you’re done with this step. You don’t need to open R yet.

---

Step 2: Install an IDE (Choose One)

What is an IDE? An Integrated Development Environment is a user-friendly application that lets you write, run, and debug R code much more easily than using R directly.

graph TB
    subgraph NoIDE["<b>WITHOUT IDE</b><br/>(Using R Console Only)"]
        direction TB
        N1["❌ Confusing interface"]
        N2["❌ Hard to organize code"]
        N3["❌ Difficult to view plots"]
        N4["❌ Tedious workflow"]
    end
    
    subgraph WithIDE["<b>WITH IDE</b><br/>(RStudio or Positron)"]
        direction TB
        Y1["✓ Clean, organized interface"]
        Y2["✓ Code editor with syntax highlighting"]
        Y3["✓ Built-in plot viewer"]
        Y4["✓ Efficient, professional workflow"]
    end
    
    style NoIDE fill:#ffccbc
    style WithIDE fill:#c8e6c9

Choose one option below:

Option A: RStudio Desktop (Recommended for Beginners)

RStudio is the most popular IDE for R. It has a clean, intuitive interface and is widely used in education and research.

Installation steps:

1. Go to the Posit website: https://posit.co/download/rstudio-desktop/

2. The website will automatically detect your operating system. Click the blue “DOWNLOAD RSTUDIO DESKTOP” button to get the free version.

3. Run the downloaded installer file:

   • Windows: Double-click the .exe file
   • macOS: Double-click the .dmg file
   • Linux: Follow the terminal instructions

4. Follow the on-screen prompts. Default settings are fine.

5. Once installation completes, you can open RStudio from your applications menu.

RStudio Interface Overview

First launch: When you open RStudio for the first time, you’ll see four panels arranged like this:

graph TB
    subgraph RStudio["<b>RStudio Layout</b>"]
        subgraph TopLeft["<b>Script Editor</b><br/>(Top-Left)"]
            TL["Where you write<br/>your R code<br/><br/>syntax highlighting<br/>code suggestions"]
        end
        
        subgraph BottomLeft["<b>Console</b><br/>(Bottom-Left)"]
            BL["Where R runs code<br/>and shows results<br/><br/>Type commands<br/>here directly"]
        end
        
        subgraph TopRight["<b>Environment/History</b><br/>(Top-Right)"]
            TR["Variables you created<br/>Previous commands<br/><br/>Track your work"]
        end
        
        subgraph BottomRight["<b>Files/Plots/Packages</b><br/>(Bottom-Right)"]
            BR["Browse files<br/>View plots<br/>Manage packages<br/>Access help"]
        end
    end
    
    style TopLeft fill:#bbdefb
    style BottomLeft fill:#fff9c4
    style TopRight fill:#f8bbd0
    style BottomRight fill:#c8e6c9

Option B: Positron (Alternative for Advanced Users)

Positron is a modern, lightweight alternative developed by Posit. It runs inside Visual Studio Code.

When to choose Positron: - You already use Visual Studio Code for other programming - You prefer a minimalist, modern interface - You want a flexible, customizable development environment

Installation steps:

1. Install VS Code (if you don’t already have it):
   • Download from https://code.visualstudio.com/
   • Run the installer and follow defaults
2. Install Positron extension:
   • Open VS Code
   • Click the Extensions icon on the left sidebar (four squares)
   • Search for Positron - R IDE
   • Click the result published by Posit and click Install
   • This will also automatically install the R extension
3. Once installation completes, restart VS Code. Positron is now ready to use.

Getting Started with Positron (Quick Guide)

graph TB
    subgraph Positron["<b>Positron Interface</b>"]
        subgraph Left["<b>Left Sidebar</b>"]
            LS["Explorer<br/>(File Browser)<br/><br/>R Icon<br/>(Environment,<br/>Plots, Help)"]
        end
        
        subgraph Center["<b>Center</b>"]
            CE["Code Editor<br/><br/>Open .R or .qmd files<br/>Write your code here"]
        end
        
        subgraph Bottom["<b>Bottom Panel</b>"]
            BT["R Console<br/>(Active Tab)<br/><br/>Run commands<br/>See results"]
        end
    end
    
    style Left fill:#e3f2fd
    style Center fill:#fff9c4
    style Bottom fill:#c8e6c9

Quick setup:

1. Open Your Project Folder:
   • Go to File > Open Folder...
   • Select the main training folder
   • The left sidebar Explorer will show all your files
2. Open the R Console:
   • Open any R file (.R or .qmd)
   • Press Ctrl+` (backtick) to open the terminal
   • Select the R tab
   • You’ll see the > prompt ready for commands
3. Run R Code:
   • Click in a line of R code
   • Press Ctrl+Enter (Windows/Linux) or Cmd+Enter (macOS)
   • Code executes in the R console below

---

Step 3: Install Required R Packages

What are packages? Packages are collections of pre-written functions that solve specific problems. Think of R as a toolbox, and packages as specialty tools inside that toolbox.

graph TB
    subgraph Core["<b>Data Wrangling</b>"]
        C1["tidyverse<br/>Filter, transform,<br/>visualize data"]
    end
    
    subgraph Assessment["<b>Stock Assessment</b>"]
        A1["LBSPR<br/>Length-based<br/>spawning potential"]
        A2["TropFishR<br/>Growth & mortality<br/>estimation"]
        A3["sizeMat<br/>Size at maturity<br/>analysis"]
    end
    
    subgraph Utilities["<b>Utilities</b>"]
        U1["readxl<br/>Read Excel files"]
        U2["janitor<br/>Clean data"]
        U3["tidyplots<br/>Easy plots"]
        U4["gt<br/>Beautiful tables"]
    end
    
    style Core fill:#bbdefb
    style Assessment fill:#c8e6c9
    style Utilities fill:#fff9c4

The packages we need:

Package	Purpose	Why It Matters
tidyverse	Data manipulation & visualization	Foundation for all analyses
LBSPR	Length-Based Spawning Potential Ratio	Core assessment method
TropFishR	Tropical fisheries stock assessment	Growth and mortality estimation
sizeMat	Size at maturity estimation	Maturity analysis
readxl	Read Excel files	Load your data
janitor	Data cleaning	Prepare data quickly
tidyplots	Professional plotting	Beautiful visualizations
gt	Create beautiful tables	Publication-ready results

Installation steps:

1. Open your IDE (RStudio or Positron).

2. Find the Console panel and copy this command:

#| eval: false
#| echo: true
#| code-summary: "Install all required packages"

install.packages(c("tidyverse", "LBSPR", "readxl", "janitor", "tidyplots", "sizeMat", "TropFishR"))

3. Paste into the console and press Enter

4. What happens next:

   • R downloads packages from the internet (5-15 minutes depending on speed)
   • You’ll see lots of text—this is normal and expected
   • R may ask about compiling from source—type No and press Enter
   • When complete, you’ll see the > prompt again

graph LR
    Start["<b>Paste Command</b><br/>into Console"] 
    Download["<b>Downloading</b><br/>5-15 minutes<br/>Normal text output"]
    Compile["<b>Installation</b><br/>May ask about<br/>compiling: Say No"]
    Complete["<b>Complete!</b><br/>See > prompt"]
    
    Start --> Download
    Download --> Compile
    Compile --> Complete
    
    style Start fill:#fff9c4
    style Download fill:#ffccbc
    style Compile fill:#fff9c4
    style Complete fill:#c8e6c9

5. Troubleshooting:
   • If you get errors about missing dependencies, run the command again
   • For individual package issues: install.packages("PackageName")
   • Internet problems? Try again or contact us

---

Step 4: Verify Your Installation

What we’re doing: Testing that everything works before training starts.

graph TB
    Start["<b>START</b><br/>Open R Console"]
    Test1["Type: library<br/>tidyverse"]
    Check1{"Error?"}
    Pass1["✓ PASS"]
    Fail1["✗ FAIL<br/>Note the error"]
    
    Test2["Type: library<br/>LBSPR"]
    Check2{"Error?"}
    Pass2["✓ PASS<br/>Ready for<br/>training!"]
    Fail2["✗ FAIL<br/>Contact us"]
    
    Start --> Test1
    Test1 --> Check1
    Check1 -->|No| Pass1
    Check1 -->|Yes| Fail1
    Pass1 --> Test2
    Test2 --> Check2
    Check2 -->|No| Pass2
    Check2 -->|Yes| Fail2
    
    style Start fill:#e1f5fe
    style Pass1 fill:#c8e6c9
    style Pass2 fill:#a5d6a7
    style Fail1 fill:#ffccbc
    style Fail2 fill:#ef9a9a

Verification steps:

1. In the R console, type these commands one at a time, pressing Enter after each:

#| eval: false
#| echo: true
#| code-summary: "Verify package installation"

library(tidyverse)
library(LBSPR)

2. Expected result:
   • Text like “Loading required package: …” without red error messages = Success!
   • Warnings (yellow text) are okay—they’re informational
   • Errors (red text starting with “Error:”) mean something is wrong
3. Troubleshooting:
   • Note the exact error message
   • Try: Session > Restart R (then test again)
   • Check your internet connection
   • Re-run the package installation command

---

You’re Ready!

graph TB
    Check1["✓ R Installed"]
    Check2["✓ IDE Installed"]
    Check3["✓ Packages Installed"]
    Check4["✓ Verified & Working"]
    
    Ready["<b>YOUR COMPUTER IS READY!</b><br/>You're set for training"]
    
    Check1 --> Ready
    Check2 --> Ready
    Check3 --> Ready
    Check4 --> Ready
    
    style Check1 fill:#c8e6c9
    style Check2 fill:#c8e6c9
    style Check3 fill:#c8e6c9
    style Check4 fill:#c8e6c9
    style Ready fill:#a5d6a7

Before training starts, please: - [ ] Verify that RStudio or Positron launches without errors - [ ] Test that you can see the R console - [ ] Run the verification commands (library commands) - [ ] Bookmark this guide for reference during training

Still having issues? Contact us before training begins with:

• Your operating system (Windows/Mac/Linux)
• The exact error messages you received
• A screenshot of the error (if possible)
• What step you’re stuck on

We’re here to help! Don’t hesitate to reach out—software setup can be tricky, and we want everyone ready to focus on stock assessment science.